I am using the Mist currently with an IBM PS/1 monitor because it is a CRT and accepts the VGA plug type. Some cores by default (Vectrex, Updated Apple II, Gameboy, CCE [Brazil] Color Computer are the main culprits) flicker like there is a refresh issue once started where it is hard to even read the menus. Are these starting in 15khz by default and my IBM monitor is not happy with it?

Found the reason of incompatibility with my TV: the core provides a composite (horizontal+verztical) 31kHz sync signal over VGA pin 13 instead of pure HSync. Discovered it accidentally, forgot to switch on my sync merger on my DIY RGB->YUV converter, and despite it the result was an acceptable picture (see screenshots). Probably it won't cause any visible difference on monitors being less picky than my TV.

Another issue may be the polarity of the sync signals: the standard says both of them should be negative at 640x480@60Hz, but i.e. in case of Apple ][ core both H and V syncs are positive. At 800x600 resolution both should be positive, but one is negative in case of GameBoy core.

You may use logical gates (members of the SN74 IC family) to reverse sync polarity, or merge them to C-Sync, but it would be more elegant solution to handle these problems on core level (but I'm not familiar with VHDL/Verilog).